I've noticed they are used in NE mirror matches, but not sure why. All they do is kill other hippogryphs which is kinda not much. Faerie Dragons and DoTs in bird form seem to be the only other targets, but it isn't like NE lacks anti-air power anyway. What am I missing?

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Hippogryphs have additional utility beyond air-to-air combat. If you have a hippogryph and an archer, you can combine the two into a hippogryph rider. The hippogryph rider has a shorter range than the archer, but are capable of ranged air-to-ground attacks that neither the hippogryph or the archer can do alone. They do the same damage as archers but are faster and can see further. This makes hippogryph riders good units for harassment, scouting, or as part of your general army composition.

The ability to morph the hippogryph/archer into the rider situationally is what makes them so powerful in any match. If your opponent has a large ground melee force, morph into riders. If they have a lot of anti-air, morph back and use your archers. If you're going against a lot of air units, attack with your hippogryphs sans riders.